After the sudden death of eleven captives marmosets in a rehabilitation center of wildlife in São Paulo, Brazil, histological and microbiological study was conducted. Liver, spleen, intestine, central nervous system, lung, thymus, stomach, testicle tissues were analyzed by light microscopy and microbial cultures were conducted. Environmental cultures were also performed. Prophylactic antimicrobial therapy, restricted access to marmosets’ cages with dedicated staff, and additional sanitization of animals’ fruits were implemented. Histological findings were compatible with hyperacute septicemia, and microbiological cultures and molecular tests identified the etiologic agent as hypermucoviscous sequence type 86 capsular type K2 K. pneumoniae for the first time in South America. Implementation of prompt containment measures led to successful control of this outbreak. Detection of a hypervirulent and zoonotic pathogen, such as hypermucoviscous K. pneumoniae ST86 K2, in an unexpected and human interface reservoir underscores its potential threat in public health settings.